Potent 5‑Cyano-6-phenyl-pyrimidin-Based Derivatives Targeting DCN1–UBE2M Interaction

Neddylation
of the Cullin-RING E3 ligases (CRLs) regulates the
homeostasis of approximately 20% of cellular proteins. Defective in
cullin neddylation 1 (DCN1), as a co-E3 ligase, interacts with UBE2M
to enhance the activation of CRLs, and this interaction is emerging
as a therapeutic target for human diseases. Here, we present a series
of pyrimidin-based small molecular inhibitors targeting DCN1–UBE2M
interaction. After finding a novel inhibitor DC-1 with
IC50 = 1.2 μM, we performed a series of chemical
optimizations, which finally led to the discovery of a potent thiazole
containing 5-cyano-6-phenylpyrimidin-based inhibitor DC-2 (IC50 = 15 nM). Next, using protein and cellular thermal
shift assays, coimmunoprecipitation, molecular docking, and site-specific
mutation experiments, we further proved that DC-2 specifically
inhibited the interaction of UBE2M and DCN1 at molecule and cellular
levels, resulting in the decrease of cullin3 neddylation and accumulation
of its substrate, NRF2. Our findings indicate that DC-2 may serve as a novel lead compound for specific derivatives targeting
DCN1–UBE2M interaction.